[med-svn] [python-pysam] 01/02: Merge branch 'master' into debian/jessie-backports

[Afif Elghraoui]

This is an automated email from the git hooks/post-receive script.

afif-guest pushed a commit to branch debian/jessie-backports
in repository python-pysam.

commit f81b19860a3adf730824bbc1357fe66464525fbb
Merge: ffc27b1 96af80c
Author: Afif Elghraoui <afif at ghraoui.name>
Date:   Fri Nov 27 11:52:54 2015 -0800

    Merge branch 'master' into debian/jessie-backports
    
    Update backport

 README.rst                                         |    5 +-
 benchmark/AlignedSegment_bench.py                  |   43 +
 debian/changelog                                   |   15 +
 debian/control                                     |    2 +-
 debian/patches/adding-include-hts-dirs             |    2 +-
 .../change-htslib-statement-to-link-to-debian      |    4 +-
 debian/patches/correct-spelling-errors.patch       |  115 -
 debian/patches/cython23.patch                      |   39 -
 .../patches/disable-tests-requiring-network.patch  |   42 +
 debian/patches/ignore-htslib-dir.patch             |    6 +-
 debian/patches/improve-python3-compatibility.patch |   27 -
 debian/patches/sam_mpileup.patch                   |   28 -
 debian/patches/series                              |    6 +-
 debian/patches/strip_online_tests.patch            |   82 -
 debian/python-pysam.lintian-overrides              |    2 +
 debian/python3-pysam.lintian-overrides             |    2 +
 debian/rules                                       |   19 +-
 debian/tests/control                               |    4 +-
 debian/watch                                       |    2 +-
 doc/api.rst                                        |   15 +-
 doc/conf.py                                        |   20 +-
 doc/faq.rst                                        |   26 +-
 doc/glossary.rst                                   |   34 +-
 doc/release.rst                                    |   86 +
 doc/usage.rst                                      |   22 +-
 pysam/TabProxies.pxd                               |   94 -
 pysam/__init__.py                                  |   64 +-
 pysam/calignedsegment.pxd                          |   94 +
 pysam/calignedsegment.pyx                          | 2277 +++++++
 pysam/calignmentfile.pxd                           |   71 +-
 pysam/calignmentfile.pyx                           | 3595 +++--------
 pysam/cbcf.pxd                                     |    2 +-
 pysam/cbcf.pyx                                     |  694 ++-
 pysam/cfaidx.pxd                                   |   54 +-
 pysam/cfaidx.pyx                                   |  470 +-
 pysam/chtslib.pxd                                  |   43 +-
 pysam/chtslib.pyx                                  |   97 +-
 pysam/csamfile.pxd                                 |    4 +-
 pysam/csamfile.pyx                                 |    2 +-
 pysam/csamtools.pxd                                |   13 +-
 pysam/csamtools.pyx                                |   63 +-
 pysam/ctabix.pxd                                   |   39 +-
 pysam/ctabix.pyx                                   |  312 +-
 pysam/ctabixproxies.pxd                            |   59 +
 pysam/{TabProxies.pyx => ctabixproxies.pyx}        |  176 +-
 pysam/cutils.pxd                                   |   27 +
 pysam/cutils.pyx                                   |  214 +
 pysam/cvcf.pxd                                     |   40 -
 pysam/cvcf.pyx                                     |  152 +-
 pysam/htslib_util.h                                |    3 -
 pysam/pysam_util.c                                 |    2 +-
 pysam/tabix_util.c                                 |    5 +-
 pysam/version.py                                   |    2 +-
 requires.txt => requirements.txt                   |    0
 save/pysam_test2.6.py                              |    2 +-
 setup.py                                           |  228 +-
 tests/AlignedSegment_test.py                       |  236 +-
 tests/AlignmentFile_test.py                        |  314 +-
 tests/SamFile_test.py                              |   74 +-
 tests/TestUtils.py                                 |    6 +-
 tests/faidx_test.py                                |   99 +-
 tests/pysam_data/Makefile                          |    2 +-
 tests/pysam_data/faidx_ex1.fa                      | 6540 ++++++++++++++++++++
 tests/pysam_data/{ex1.fq => faidx_ex1.fq}          |    0
 tests/samtools_test.py                             |   93 +-
 tests/tabix_test.py                                |   46 +-
 66 files changed, 12616 insertions(+), 4340 deletions(-)

diff --cc debian/changelog
index 754150a,cb331b8..6b85ed9
--- a/debian/changelog
+++ b/debian/changelog
@@@ -1,10 -1,18 +1,25 @@@
+ python-pysam (0.8.4+ds-1) unstable; urgency=medium
+ 
+   * Add version constraints to build-dependencies.
+   * Drop ds suffix versioning.
+   * Imported Upstream version 0.8.4+ds
+   * Remove patches applied upstream
+   * Refresh existing patches
+   * Refine d/rules
+   * Set Vcs-Browser to point to cgit rather than gitweb
+   * Reduce dependencies in autopktest dependencies
+   * Replace patch for network-dependent tests
+   * Add new lintian overrides
+ 
+  -- Afif Elghraoui <afif at ghraoui.name>  Fri, 13 Nov 2015 22:15:14 -0800
+ 
 +python-pysam (0.8.3+ds1-3~bpo8+1) jessie-backports; urgency=medium
 +
 +  * Add version constraints for build-depends.
 +  * Rebuild for jessie-backports.
 +
 + -- Afif Elghraoui <afif at ghraoui.name>  Fri, 23 Oct 2015 20:24:03 -0700
 +
  python-pysam (0.8.3+ds1-3) unstable; urgency=medium
  
    * Backport upstream commit 6efb22b to permit building with Cython 0.23.x

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